SRR3403688	GSE80451	GSM2127619	GPL14548	PMID_28103245	Aerobic 3	Transcriptome analysis of E. coli REL4536 grown aerobically and anaerobically	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	data_processing	Sequence data from BGI had been filtered to remove reads containing ≥ 10% unreadable bases, ≥ 20% low quality (≤ Q20) bases, adapter contamination or duplicate read-pairs PGCGROWTHCONDITIONS
SRR3403688	GSE80451	GSM2127619	GPL14548	PMID_28103245	Aerobic 3	Transcriptome analysis of E. coli REL4536 grown aerobically and anaerobically	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	data_processing	The quality of reads was assessed by using FastQC (Andrews S, 2010) and any reads with a quality score ≤  Q28 were trimmed using Trim Galore! (Krueger F, 2013 ). PGCGROWTHCONDITIONS
SRR3403688	GSE80451	GSM2127619	GPL14548	PMID_28103245	Aerobic 3	Transcriptome analysis of E. coli REL4536 grown aerobically and anaerobically	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	data_processing	Bowtie 2 (Langmead B & Salzberg SL, 2012) was used with default parameters, to remove any sequence reads aligning to ribosomal RNA, transfer RNA and non-coding RNA sequences. PGCGROWTHCONDITIONS
SRR3403688	GSE80451	GSM2127619	GPL14548	PMID_28103245	Aerobic 3	Transcriptome analysis of E. coli REL4536 grown aerobically and anaerobically	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	data_processing	RNA-Seq reads were mapped to the reference genome using EDGE-Pro (Magoc T, Wood D and Salzberg SL, 2013) ) with default parameters PGCGROWTHCONDITIONS
SRR3403688	GSE80451	GSM2127619	GPL14548	PMID_28103245	Aerobic 3	Transcriptome analysis of E. coli REL4536 grown aerobically and anaerobically	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	data_processing	Differential expression between aerobic and anaerobic environments was identified by using DESeq2 (Love M, Huber W and  Anders S, 2014) PGCGROWTHCONDITIONS
SRR3403688	GSE80451	GSM2127619	GPL14548	PMID_28103245	Aerobic 3	Transcriptome analysis of E. coli REL4536 grown aerobically and anaerobically	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	data_processing	Genome_build: Escherichia coli B str. REL606; NC_012967.1 PGCGROWTHCONDITIONS
SRR3403688	GSE80451	GSM2127619	GPL14548	PMID_28103245	Aerobic 3	Transcriptome analysis of E. coli REL4536 grown aerobically and anaerobically	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	data_processing	Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample PGCGROWTHCONDITIONS
SRR3403688	GSE80451	GSM2127619	GPL14548	PMID_28103245	Aerobic 3	Transcriptome analysis of E. coli REL4536 grown aerobically and anaerobically	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	extract_protocol	RNA was extracted from harvested cultures using a hot lysis buffer and acid phenol-based extraction method and isopropanol precipitation. Following RNA extraction, Turbo DNase (Ambion, USA) was used to treat the samples as per manufacturer’s instructions. Each sample was split into five 20 μL aliquots and two rounds of DNase treatment were performed on each aliquot. Following DNase treatment, RNA samples were purified using the RNeasy Mini kit (Qiagen, Germany) as per the manufacturer’s instructions. For each sample, the DNase-treated aliquots were pooled together before purification. RNA quality was measured using the Agilent 2100 Bioanalyzer (Agilent Technologies, USA) with the RNA 6000 Nano Chip kit according to the manufacturer’s instructions while RNA was quantified using the Quant-iT RNA Assay kit (Life Technologies) and measured on a Qubit® 2.0 fluorometer. RNA was sequenced on the Illumina HiSeq 2000 platform  at BGI (Shenzen, China). PGCGROWTHCONDITIONS
SRR3403688	GSE80451	GSM2127619	GPL14548	PMID_28103245	Aerobic 3	Transcriptome analysis of E. coli REL4536 grown aerobically and anaerobically	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	extract_protocol	RNA libraries were prepared for sequencing using standard Illumina protocols PGCGROWTHCONDITIONS
SRR3403688	GSE80451	GSM2127619	GPL14548	PMID_28103245	Aerobic 3	Transcriptome analysis of E. coli REL4536 grown aerobically and anaerobically	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	Aerobic and anaerobic cultures were grown in 600 mL aliquots of DM25 and incubated at 37°C with an orbital shaking of 150 RPM and inoculated with 1/100th volume of overnight culture. Aerobic cultures were grown for 9 h while anaerobic cultures were grown for 16 h. PGCGROWTHCONDITIONS
SRR3403688	GSE80451	GSM2127619	GPL14548	PMID_28103245	Aerobic 3	Transcriptome analysis of E. coli REL4536 grown aerobically and anaerobically	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	organism	Escherichia coli PGCGROWTHCONDITIONS
SRR3403688	GSE80451	GSM2127619	GPL14548	PMID_28103245	Aerobic 3	Transcriptome analysis of E. coli REL4536 grown aerobically and anaerobically	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	source_name	Cultured cells PGCGROWTHCONDITIONS
SRR3403688	GSE80451	GSM2127619	GPL14548	PMID_28103245	Aerobic 3	Transcriptome analysis of E. coli REL4536 grown aerobically and anaerobically	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	library_strategy	RNA-Seq PGCGROWTHCONDITIONS
SRR3403688	GSE80451	GSM2127619	GPL14548	PMID_28103245	Aerobic 3	Transcriptome analysis of E. coli REL4536 grown aerobically and anaerobically	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	characteristics	strain: REL4536 PGCGROWTHCONDITIONS
SRR3403688	GSE80451	GSM2127619	GPL14548	PMID_28103245	Aerobic 3	Transcriptome analysis of E. coli REL4536 grown aerobically and anaerobically	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	characteristics	growth phase: Stationary phase PGCGROWTHCONDITIONS
SRR3403688	GSE80451	GSM2127619	GPL14548	PMID_28103245	Aerobic 3	Transcriptome analysis of E. coli REL4536 grown aerobically and anaerobically	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	characteristics	growth environment: Aerobic PGCGROWTHCONDITIONS
SRR3403688	GSE80451	GSM2127619	GPL14548	PMID_28103245	Aerobic 3	Transcriptome analysis of E. coli REL4536 grown aerobically and anaerobically	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	Aerobic and anaerobic cultures were grown in 600 mL aliquots of DM25 and incubated at 37°C with an orbital shaking of 150 RPM and inoculated with 1/100th volume of overnight culture. Aerobic cultures were grown for 9 h while anaerobic cultures were grown for 16 h. PGCGROWTHCONDITIONS
SRR3403688	GSE80451	GSM2127619	GPL14548	PMID_28103245	Aerobic 3	Transcriptome analysis of E. coli REL4536 grown aerobically and anaerobically	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	organism	Escherichia coli PGCGROWTHCONDITIONS
SRR3403688	GSE80451	GSM2127619	GPL14548	PMID_28103245	Aerobic 3	Transcriptome analysis of E. coli REL4536 grown aerobically and anaerobically	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	source_name	Cultured cells PGCGROWTHCONDITIONS
SRR3403688	GSE80451	GSM2127619	GPL14548	PMID_28103245	Aerobic 3	Transcriptome analysis of E. coli REL4536 grown aerobically and anaerobically	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	contact_name	Christina,,Moon PGCGROWTHCONDITIONS